Contacts of the strand formed by residues 102 - 107 (chain K) in PDB entry 1FSK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 102 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K GLN* 3.4 24.7 - - + +
7K SER 5.0 1.6 - - - +
8K PRO* 2.7 29.7 + - - +
9K LYS 3.5 7.0 + - - -
10K SER* 4.1 5.2 + - - -
11K MET* 4.8 0.2 - - - +
21K LEU* 3.3 39.6 - - + +
22K SER 5.4 1.8 - - - +
85K ASP* 3.2 3.9 + - - -
86K TYR* 3.1 28.3 + - + +
101K GLY* 1.3 74.1 - - - -
103K LYS* 1.3 62.6 + - - +
104K LEU 3.5 1.9 + - - -
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Residues in contact with LYS 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K LYS 3.2 11.9 + - - +
10K SER* 3.3 8.4 - - - -
11K MET* 2.9 27.1 + - - +
21K LEU* 6.1 0.2 - - - -
83K LEU* 5.6 3.4 - - + -
84K ALA 3.7 13.0 - - - +
85K ASP* 3.6 14.1 + - + +
101K GLY 4.2 0.2 - - - -
102K THR* 1.3 70.5 - - - +
104K LEU* 1.3 65.1 + - - +
105K GLU* 3.6 39.3 + - + +
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Residues in contact with LEU 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K MET* 3.7 22.4 - - + +
13K VAL* 4.6 7.9 - - + -
19K VAL* 4.3 24.5 - - + -
21K LEU* 5.4 6.3 - - + -
75K ILE* 4.0 20.0 - - + -
78K VAL* 4.0 18.8 - - + -
82K ASP 3.2 23.8 - - - +
83K LEU* 2.7 33.3 - - - +
84K ALA 2.8 19.1 + - - +
86K TYR* 3.7 18.2 - - + -
102K THR 3.5 1.8 + - - +
103K LYS* 1.3 73.7 - - - +
105K GLU* 1.3 58.3 + - - +
106K ILE* 4.3 1.1 - - + -
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Residues in contact with GLU 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K SER* 3.7 23.4 + - - -
11K MET 2.6 16.1 + - - +
12K SER* 2.9 41.7 + - - +
13K VAL* 3.1 5.4 + - - +
83K LEU* 4.0 1.1 - - + -
103K LYS* 3.6 38.7 + - + +
104K LEU* 1.3 78.5 - - - +
106K ILE* 1.3 64.0 + - - +
166K GLN* 3.7 10.7 - - - +
173K TYR* 4.0 14.8 + - - +
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Residues in contact with ILE 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K SER* 5.6 0.9 - - - -
13K VAL* 3.2 9.6 - - + +
15K VAL* 3.9 20.0 - - + +
78K VAL* 4.5 10.5 - - + -
79K GLN 3.1 13.2 - - - +
80K ALA* 3.1 43.7 - - - +
83K LEU* 4.0 17.2 - - + +
104K LEU* 4.4 2.2 + - + -
105K GLU* 1.3 73.9 - - - +
107K LYS* 1.3 73.8 + - - +
108K ARG* 4.2 0.4 + - + -
140K TYR* 3.7 2.4 + - - -
166K GLN* 2.3 39.6 + - - +
171K SER* 3.4 24.9 - - - +
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Residues in contact with LYS 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K SER* 5.0 8.3 - - - +
13K VAL* 2.8 21.1 + - - +
14K SER* 3.5 35.6 + - - +
15K VAL* 4.2 3.3 + - - +
105K GLU 3.9 0.2 + - - -
106K ILE* 1.3 77.4 - - - +
108K ARG* 1.3 73.6 + - - +
140K TYR* 3.0 16.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il